A tuber mustard AP2/ERF transcription factor gene, BjABR1, functioning in abscisic acid and abiotic stress responses, and evolutionary trajectory of the ABR1 homologous genes in Brassica species

The AP2/ERF superfamily of transcription factors is one of the largest transcription factor families in plants and plays an important role in plant development processes and stress responses. In this study, BjABR1, an AP2/ERF superfamily gene, from tuber mustard (Brassica juncea var. tumida Tsen et Lee), sharing high amino acid sequence similarity with the AtABR1 (Arabidopsis thaliana AP2-like abscisic acid repressor 1) gene, were performed functional research, and the ABR1 homologous genes in Brassica species were identified and performed phylogenetic analysis. The promoter sequence of BjABR1 contained many phytohormone- and stress-related cis-elements; ABA (abscisic acid) and abiotic stresses can induce BjABR1 expression in tuber mustard; overexpression of BjABR1 in Arabidopsis can alleviate plant sensitivity to ABA and salt and osmotic stresses, and the alleviation may be due to changes in stress/ABA-induced gene expression. These results indicated that BjABR1 functions in ABA and abiotic stress responses. By BLAST searches against the genome database of five Brassica species (three diploids, B. rapa, B. nigra, and B. oleracea, and two allotetraploid, B. juncea and B. napus) using the protein sequence of AtABR1, 3, 3, 3, 6, and 5 ABR1 homologous genes in B. nigra, B. rapa, B. oleracea, B. juncea, and B. napus were identified, respectively, and they shared high sequence similarity. By sequence analysis, annotation mistakes of the protein-coding regions of two ABR1 homologous genes, GSBRNA2T00134741001 and BjuB007684, were found and corrected. Then, the evolution analysis of these ABR1 homologous genes showed that the ancestor of the three diploid species had three ABR1 homologous genes and each diploid inherited all the three genes from their ancestor; then, allotetraploid B. juncea inherited all the six genes from B. rapa and B. nigra with no gene lost, while allotetraploid B. napus inherited all the three genes from B. oleracea and two genes from B. rapa with one gene lost, indicating that ABR1 homologous genes possessed greater hereditary conservation in Brassica species. The ABR1 homologous genes between B. rapa and B. oleracea shared much higher sequence similarity compared to that of B. nigra in diploid species, indicating that ABR1 homologous genes in B. nigra had experienced more rapid evolution, and B. rapa and B. oleracea may share closer relationship compared to B. nigra. Moreover, the spatial and temporal expression analysis of six ABR1 homologous genes of tuber mustard showed that they possessed different expression models. These results imply that ABR1 homologous genes are important to Brassica plants, and they may possess similar function in ABA and abiotic stress responses but play a role in different tissues and growing stages of plant. This study will provide the foundation to the functional research of ABR1 homologous genes in the Brassica species and help to reveal and understand the evolution mechanisms of Brassica species

Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development

Cotton plant architecture, including fruit branch formation and flowering pattern, influences plant light exploitation, cotton yield and planting cost. DNA methylation has been widely observed at different developmental stages in both plants and animals and is associated with regulation of gene expression, chromatin remodelling, genome protection and other functions. Here, we investigated the global epigenetic reprogramming during the development of fruiting branches and floral buds at three developmental stages: the seedling stage, the pre-squaring stage and the squaring stage. We first identified 22 cotton genes which potentially encode DNA methyltransferases and demethylases. Among them, the homologous genes of CMT, DRM2 and MET1 were upregulated at pre-squaring and squaring stages, suggesting that DNA methylation is involved in the development of floral buds and fruit branches. Although the global methylation at all of three developmental stages was not changed, the CHG-type methylation of non-expressed genes was higher than those of expressed genes. In addition, we found that the expression of the homologous genes of the key circadian rhythm regulators, including CRY, LHY and CO, was associated with changes of DNA methylation at three developmental stages

Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing

<p>Abstract</p> <p>Background</p> <p>Tumourous stem mustard (<it>Brassica juncea </it>var. <it>tumida </it>Tsen et Lee) is an economically and nutritionally important vegetable crop of the <it>Cruciferae </it>family that also provides the raw material for <it>Fuling </it>mustard. The genetics breeding, physiology, biochemistry and classification of mustards have been extensively studied, but little information is available on tumourous stem mustard at the molecular level. To gain greater insight into the molecular mechanisms underlying stem swelling in this vegetable and to provide additional information for molecular research and breeding, we sequenced the transcriptome of tumourous stem mustard at various stem developmental stages and compared it with that of a mutant variety lacking swollen stems.</p> <p>Results</p> <p>Using Illumina short-read technology with a tag-based digital gene expression (DGE) system, we performed <it>de novo </it>transcriptome assembly and gene expression analysis. In our analysis, we assembled genetic information for tumourous stem mustard at various stem developmental stages. In addition, we constructed five DGE libraries, which covered the strains <it>Yong'an </it>and <it>Dayejie </it>at various development stages. Illumina sequencing identified 146,265 unigenes, including 11,245 clusters and 135,020 singletons. The unigenes were subjected to a BLAST search and annotated using the GO and KO databases. We also compared the gene expression profiles of three swollen stem samples with those of two non-swollen stem samples. A total of 1,042 genes with significantly different expression levels occurring simultaneously in the six comparison groups were screened out. Finally, the altered expression levels of a number of randomly selected genes were confirmed by quantitative real-time PCR.</p> <p>Conclusions</p> <p>Our data provide comprehensive gene expression information at the transcriptional level and the first insight into the understanding of the molecular mechanisms and regulatory pathways of stem swelling and development in this plant, and will help define new mechanisms of stem development in non-model plant organisms.</p

Functional analysis of the GbDWARF14 gene associated with branching development in cotton

Plant architecture, including branching pattern, is an important agronomic trait of cotton crops. In recent years, strigolactones (SLs) have been considered important plant hormones that regulate branch development. In some species such as Arabidopsis, DWARF14 is an unconventional receptor that plays an important role in the SL signaling pathway. However, studies on SL receptors in cotton are still lacking. Here, we cloned and analysed the structure of the GbD14 gene in Gossypium barbadense and found that it contains the domains necessary for a SL receptor. The GbD14 gene was expressed primarily in the roots, leaves and vascular bundles, and the GbD14 protein was determined via GFP to localize to the cytoplasm and nucleus. Gene expression analysis revealed that the GbD14 gene not only responded to SL signals but also was differentially expressed between cotton plants whose types of branching differed. In particular, GbD14 was expressed mainly in the axillary buds of normal-branching cotton, while it was expressed the most in the leaves of nulliplex-branch cotton. In cotton, the GbD14 gene can be induced by SL and other plant hormones, such as indoleacetic acid, abscisic acid, and jasmonic acid. Compared with wild-type Arabidopsis, GbD14-overexpressing Arabidopsis responded more rapidly to SL signals. Moreover, we also found that GbD14 can rescue the multi-branched phenotype of Arabidopsis Atd14 mutants. Our results indicate that the function of GbD14 is similar to that of AtD14, and GbD14 may be a receptor for SL in cotton and involved in regulating branch development. This research provides a theoretical basis for a profound understanding of the molecular mechanism of branch development and ideal plant architecture for cotton breeding improvements

Glandless seed and glanded plant research in cotton. A review

Recently the world has been entangled by insufficient food such as the lack of rice which threatens the safety of world food and affect sustainable development of the world economy, resulting in rising of food price. To address this issue, cotton appears as a possible source of both fiber and food. The research in recent years indeed showed bright prospects for this expectation. However, gossypol stored in the glands of cotton is toxic to nonruminant animals and humans, which wastes large amounts of cottonseed protein that could potentially provide the annual protein requirements for half a billion people. Gossypium species are characterized by their lysigenous glands containing terpenoid aldehydes, important secondary phytoalexins consisting mainly of gossypol, which constitute one of the important plant’s defense system against pests and diseases. The best approach to address this issue is to create glandless seed and glanded plant cotton. A breakthrough in this field would realise the fulfilment of making cotton both a fiber and a food crop, which would be a feat of great magnitude for sustainable development of agriculture. Research on the relationship between glands and their secondary inclusions at the molecular level would be one approach for genetic engineering to control the glands and gossypol content. In this article, we review recent progress on glands and gossypol content for diverse gland types in Gossypium species, inheritance of glands and gossypol content, traditional breeding of glandless seeds and glanded plant cotton, the terpenoid aldehyde biosynthesis pathway, molecular cloning of the related genes, the strategy for genetic engineering, and future prospects

Study on the mechanical and thermal properties of one-part geopolymer composite for high performance in energy piles

One-part geopolymer is a single-component, easy-to-use geopolymer material that offers simplified and cost-effective production processes for eco-friendly building materials. This study aimed to optimize the thermal and mechanical properties of one-part geopolymer for geothermal energy applications by incorporating both silicon carbide (SiC) sand and SiC powder. Various mix designs of one-part geopolymer composites were investigated, and their flexural and compressive strength were analysed. Thermal conductivity was measured using a novel home-made test set-up. Results showed that the compressive strength of one-part geopolymer composite can be as high as 83 MPa under ambient curing condition. The relationship between flexural and compressive strength was also studied, with the PCA code providing the best fitting precision. Furthermore, the thermal conductivity of one-part geopolymer composite was significantly increased with the combined application of SiC powder and SiC particles. These findings suggest that geopolymer composites with SiC materials are suitable for geothermal energy applications

Additional file 7: Table S5. of Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species

The amino acid sequence similarity between G. arboretum NBS genes and G. barbadense NBS genes. (XLS 1475 kb

Additional file 2: Table S9. of Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species

Exon statistics in NBS genes and each NBS gene type in the four cotton species. (XLSX 9 kb

Additional file 6: Table S4. of Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species

The amino acid sequence similarity between G. raimondii NBS genes and G. hirsutum NBS genes. (XLS 2569 kb

Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq

Circular RNAs (circRNAs), a class of recently discovered non-coding RNAs, play a role in biological and developmental processes. A recent study showed that circRNAs exist in plants and play a role in their environmental stress responses. However, cotton circRNAs and their role in Verticillium wilt response have not been identified up to now. In this study, two CSSLs (chromosome segment substitution lines) of G.barbadense introgressed into G. hirsutum, CSSL-1 and CSSL-4 (a resistant line and a susceptible line to Verticillium wilt, respectively), were inoculated with V. dahliae for RNA-seq library construction and circRNA analysis. A total of 686 novel circRNAs were identified. CSSL-1 and CSSL-4 had similar numbers of circRNAs and shared many circRNAs in common. However, CSSL-4 differentially expressed approximately twice as many circRNAs as CSSL-1, and the differential expression levels of the common circRNAs were generally higher in CSSL-1 than in CSSL-4. Moreover, two C-RRI comparisons, C-RRI-vs-C-RRM and C-RRI-vs-C-RSI, possessed a large proportion (approximately 50%) of the commonly and differentially expressed circRNAs. These results indicate that the differentially expressed circRNAs may play roles in the Verticillium wilt response in cotton. A total of 280 differentially expressed circRNAs were identified. A Gene Ontology analysis showed that most of the ‘stimulus response’ term source genes were NBS family genes, of which most were the source genes from the differentially expressed circRNAs, indicating that NBS genes may play a role in Verticillium wilt resistance and might be regulated by circRNAs in the disease-resistance process in cotton